Cherno More captain Mihail Venkov was hit by what appeared to be a tin can just before the break.
The second half was also delayed by several minutes after Levski fans threw flares and firecrackers on the pitch.
Just after the final whistle Levski supporters set seats on fire and threw them on to the field before riot police restored order.
Levski went ahead after 72 minutes through Spanish midfielder Antonio Anete but his compatriot Bacari levelled in the third minute of added time and Martinique winger Mathias Coureur grabbed the winner in the 119th minute.
The two teams ended with 10 men after Cherno More’s Cape Verde midfielder Stenio and Levski defender Veselin Minev were sent off.
(Reporting by Angel Krasimirov, editing by Tony Jimenez)
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